Thiazotropsin aggregation and its relationship to molecular recognition in the DNA minor groove

Marie-Virginie Salvia, Fiona Addison, Hasan Y H Alniss, Niklaas J Buurma, Abedawn Khalaf, Simon MacKay, Nahoum G Anthony, Colin Suckling, Maxim P Evstigneev, Adrian Hernandez Santiago, Roger Waigh, John Parkinson

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Abstract

Aggregated states have been alluded to for many DNA minor groove binders but details of the molecule-on-molecule relationship have either been under-reported or ignored. Here we report our findings from ITC and NMR measurements carried out with AIK-18/51, a compound representative of the thiazotropsin class of DNA minor groove binders. The free aqueous form of AIK-18/51 is compared with that found in its complex with cognate DNA duplex d(CGACTAGTCG)2. Molecular self-association of AIK-18/51 is consistent with anti-parallel, face-to-face dimer formation, the building block on which the molecule aggregates. This underlying structure is closely allied to the form found in the ligand’s DNA complex. NMR chemical shift and diffusion measurements yield a self-association constant Kass = (61 ± 19) × 103 M- 1 for AIK-18/51 that fits with a stepwise self-assembly model and is consistent with ITC data. The deconstructed energetics of this assembly process are reported with respect to a design strategy for ligand/DNA recognition.
Original languageEnglish
Pages (from-to)1-11
Number of pages11
JournalBiophysical Chemistry
Volume179
Early online date25 Apr 2013
DOIs
Publication statusPublished - Sep 2013

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Keywords

  • ligand-assembly
  • aggregation
  • ITC
  • NMR
  • self-diffusion
  • molecular recognition
  • DNA minor groove

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